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# Ribosome Stalling - Usage Guide
## Overview
Detect ribosome pausing and stalling sites at codon resolution to study translational regulation, rare codon effects, and nascent chain interactions.
## Prerequisites
```bash
pip install plastid numpy scipy biopython
```
## Quick Start
Tell your AI agent:
- "Find ribosome pause sites in my Ribo-seq data"
- "Calculate codon-specific ribosome occupancy"
- "Identify stalling at rare codons"
- "Analyze pause motifs"
## Example Prompts
### Pause Site Detection
> "Find positions with elevated ribosome occupancy (z-score > 3)"
> "Identify stalling sites in my genes of interest"
> "How many pause sites are there per gene?"
### Codon Analysis
> "Calculate average ribosome occupancy per codon"
> "Which codons have highest pause frequency?"
> "Correlate pausing with tRNA abundance"
### Motif Analysis
> "What amino acid motifs are enriched at pause sites?"
> "Find polyproline-associated stalling"
> "Analyze context around pause sites"
## What the Agent Will Do
1. Map reads to P-site positions using offset
2. Calculate codon-level ribosome occupancy
3. Identify positions with elevated occupancy (z-score)
4. Aggregate by codon type
5. Analyze sequence/motif context
## Tips
- **Correct P-site offset** is critical for codon assignment
- **Z-score > 3** is a typical threshold for pause sites
- **Normalize by gene expression** to compare across genes
- **Polyproline** (PPP) is a well-known pause motif
- **Rare codons** correlate with pausing (tRNA limitation)
